GUSB and ATP2B4 are suitable reference genes for CFTR gene expression data normalization in nasal epithelium cells

Journal of Cystic Fibrosis

Volumn 11, Issue 5, 2012, Pages 398-404

  Masvidal, Laia ^a   Alvarez, Antoni ^b   Ruano, Laura ^b   de Gracia, Javier ^b   Larriba, Sara ^a   Casals, Teresa ^a  

^a BELLVITGE BIOMEDICAL RESEARCH INSTITUTE IDIBELL   (Spain)

^b HOSPITAL UNIVERSITARI VALL D HEBRON   (Spain)

Author keywords

CFTR; Cystic fibrosis; Gene expression; Nasal epithelium; Reference gene; RT qPCR

Indexed keywords

COMPLEMENTARY DNA;

ARTICLE; BETA 2 MICROGLOBULIN GENE; CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR GENE; EPITHELIUM CELL; GENE; GENE EXPRESSION; GLUCURONIDASE BETA GENE; HUMAN; HUMAN CELL; HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE 1 GENE; NOSE MUCOSA; NUCLEOTIDE SEQUENCE; PLASMA MEMBRANE CALCIUM TRANSPORTING ATPASE 4 GENE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

ADULT; BETA 2-MICROGLOBULIN; CYSTIC FIBROSIS; CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR; GENE EXPRESSION PROFILING; GLUCURONIDASE; HUMANS; ION TRANSPORT; NASAL MUCOSA; PLASMA MEMBRANE CALCIUM-TRANSPORTING ATPASES; REFERENCE VALUES; REPRODUCIBILITY OF RESULTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

EID: 84866175784     PISSN: 15691993     EISSN: 18735010     Source Type: Journal    
DOI: 10.1016/j.jcf.2012.03.008     Document Type: Article

References (29)

1. Castellani C., Cuppens H., Macek M., et al. Consensus on the use and interpretation of cystic fibrosis mutation analysis in clinical practice. J Cyst Fibros 2008, 7(3):179-196.
2. Larriba S., Bassas L., Gimenez J., et al. Testicular CFTR splice variants in patients with congenital absence of the vas deferens. Hum Mol Genet 1998, 7(11):1739-1743.
3. Chiba-Falek O., Parad R.B., Kerem E., Kerem B. Variable levels of normal RNA in different fetal organs carrying a cystic fibrosis transmembrane conductance regulator splicing mutation. Am J Respir Crit Care Med 1999, 159(6):1998-2002.
4. Andrieux J., Audrezet M.P., Frachon I., et al. Quantification of CFTR splice variants in adults with disseminated bronchiectasis, using the TaqMan fluorogenic detection system. Clin Genet 2002, 62(1):60-67.
5. Ramalho A.S., Beck S., Meyer M., Penque D., Cutting G.R., Amaral M.D. Five percent of normal cystic fibrosis transmembrane conductance regulator mRNA ameliorates the severity of pulmonary disease in cystic fibrosis. Am J Respir Cell Mol Biol 2002, 27(5):619-627.
6. Ginzinger D.G. Gene quantification using real-time quantitative PCR: an emerging technology hits the mainstream. Exp Hematol 2002, 30(6):503-512.
7. Bustin S.A., Benes V., Garson J.A., et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 2009, 55(4):611-622.
8. Fleige S., Pfaffl M.W. RNA integrity and the effect on the real-time qRT-PCR performance. Mol Aspects Med 2006, 27(2-3):126-139.
9. Vandesompele J., De Preter K., Pattyn F., et al. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 2002, 3(7). [RESEARCH0034].
10. Aerts J.L., Gonzales M.I., Topalian S.L. Selection of appropriate control genes to assess expression of tumor antigens using real-time RT-PCR. Biotechniques 2004, 36(1):84-91.
11. Hruz T., Wyss M., Docquier M., et al. RefGenes: identification of reliable and condition specific reference genes for RT-qPCR data normalization. BMC Genomics 2011, 12:156-169.
12. Huggett J., Dheda K., Bustin S., Zumla A. Real-time RT-PCR normalisation; strategies and considerations. Genes Immun 2005, 6(4):279-284.
13. Dheda K, Huggett JF, Bustin SA, Johnson MA, Rook G, Zumla A. Validation of housekeeping genes for normalizing RNA expression in real-time PCR. Biotechniques 2004;37(1):112-4, 116, 118-9.
14. Dheda K., Huggett J.F., Chang J.S., et al. The implications of using an inappropriate reference gene for real-time reverse transcription PCR data normalization. Anal Biochem 2005, 344(1):141-143.
15. Gene G.G., Llobet A., Larriba S., et al. N-terminal CFTR missense variants severely affect the behavior of the CFTR chloride channel. Hum Mutat 2008, 29(5):738-749.
16. Schroeder A., Mueller O., Stocker S., et al. The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC Mol Biol 2006, 7:3.
17. Calcagno A.M., Chewning K.J., Wu C.P., Ambudkar S.V. Plasma membrane calcium ATPase (PMCA4): a housekeeper for RT-PCR relative quantification of polytopic membrane proteins. BMC Mol Biol 2006, 7:29.
18. Hellemans J., Mortier G., De Paepe A., Speleman F., Vandesompele J. qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol 2007, 8(2):R19.
19. Andersen C.L., Jensen J.L., Orntoft T.F. Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res 2004, 64(15):5245-5250.
20. de Kok J.B., Roelofs R.W., Giesendorf B.A., et al. Normalization of gene expression measurements in tumor tissues: comparison of 13 endogenous control genes. Lab Invest 2005, 85(1):154-159.
21. Hsiao L.L., Dangond F., Yoshida T., et al. A compendium of gene expression in normal human tissues. Physiol Genomics 2001, 7(2):97-104.
22. Bustin S.A., Nolan T. Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction. J Biomol Tech 2004, 15(3):155-166.
23. Tricarico C., Pinzani P., Bianchi S., et al. Quantitative real-time reverse transcription polymerase chain reaction: normalization to rRNA or single housekeeping genes is inappropriate for human tissue biopsies. Anal Biochem 2002, 309(2):293-300.
24. Coulson D.T., Brockbank S., Quinn J.G., et al. Identification of valid reference genes for the normalization of RT qPCR gene expression data in human brain tissue. BMC Mol Biol 2008, 9:46.
25. Fu L.Y., Jia H.L., Dong Q.Z., et al. Suitable reference genes for real-time PCR in human HBV-related hepatocellular carcinoma with different clinical prognoses. BMC Cancer 2009, 9:49.
26. Fassunke J., Blum M.C., Schildhaus H.U., et al. qPCR in gastrointestinal stromal tumors: Evaluation of reference genes and expression analysis of KIT and the alternative receptor tyrosine kinases FLT3, CSF1-R, PDGFRB. MET and AXL. BMC Mol Biol 2010, 11:100.
27. Applied-Biosystems ABI Prism Bulletin #2 2001.
28. Willems E., Leyns L., Vandesompele J. Standardization of real-time PCR gene expression data from independent biological replicates. Anal Biochem 2008, 379(1):127-129.
29. Willems E., Mateizel I., Kemp C., Cauffman G., Sermon K., Leyns L. Selection of reference genes in mouse embryos and in differentiating human and mouse ES cells. Int J Dev Biol 2006, 50(7):627-635.